Branch:
user/anddt/network/znc
11.0
12.0
12.1
12.2
13.0
13.1
13.37
14.0
14.1
14.2
15.0
bedlam
bedlam-name-fixes
dive
erik
gitignore
libressl-gopher-test
master
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python-renames
rworkman
urchlay
user/aclemons/updates
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user/anddt/development/glm
user/anddt/development/gnustep-base
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user/anddt/network/sshguard
user/anddt/network/strongswan
user/anddt/network/umurmur
user/anddt/network/yt-dlp
user/anddt/network/znc
user/anddt/office/gnumeric
user/anddt/office/sigil
user/anddt/system/FontAwesome
user/anddt/system/conky
user/anddt/system/fakeroot
user/anddt/system/hplip-plugin
user/anddt/system/postgresql
user/anddt/system/testdisk
user/anddt/system/worker
user/anddt/system/xen
user/anddt/system/zzzfm
user/belka/updates
user/chris.willing/updates
user/dslackw/updates
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user/kingbeowulf/updates
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willysr
wxWidgets-wip
GPG-KEY
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Andrew Clemons
825a298531
academic/trimmomatic: Use zulu-openjdk11.
|
2 years ago | |
|---|---|---|
| .. | ||
| README | f80572fa0f academic/trimmomatic: Added (Trimming Tool). | 5 years ago |
| References | f80572fa0f academic/trimmomatic: Added (Trimming Tool). | 5 years ago |
| slack-desc | f80572fa0f academic/trimmomatic: Added (Trimming Tool). | 5 years ago |
| trimmomatic.SlackBuild | 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var | 2 years ago |
| trimmomatic.info | 825a298531 academic/trimmomatic: Use zulu-openjdk11. | 2 years ago |
README
Trimmomatic: A flexible read trimming tool for Illumina NGS data
Trimmomatic performs a variety of useful trimming tasks for illumina
paired-end and single ended data.The selection of trimming steps and
their associated parameters are supplied on the command line.
The current trimming steps are:
- ILLUMINACLIP: Cut adapter and other illumina-specific sequences from
the read.
- SLIDINGWINDOW: Perform a sliding window trimming, cutting once the
average quality within the window falls below a threshold.
- LEADING: Cut bases off the start of a read, if below a threshold
quality
- TRAILING: Cut bases off the end of a read, if below a threshold
quality
- CROP: Cut the read to a specified length
- HEADCROP: Cut the specified number of bases from the start of the
read
- MINLEN: Drop the read if it is below a specified length
- TOPHRED33: Convert quality scores to Phred-33
- TOPHRED64: Convert quality scores to Phred-64
It works with FASTQ (using phred + 33 or phred + 64 quality scores,
depending on the Illumina pipeline used), either uncompressed or
gzipp'ed FASTQ. Use of gzip format is determined based on the .gz
extension.
For single-ended data, one input and one output file are specified,
plus the processing steps. For paired-end data, two input files are
specified, and 4 output files, 2 for the 'paired' output where both
reads survived the processing, and 2 for corresponding 'unpaired'
output where a read survived, but the partner read did not.
Citations
Bolger, A. M., Lohse, M., & Usadel, B. (2014).
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bioinformatics, btu170.
Trimmomatic performs a variety of useful trimming tasks for illumina
paired-end and single ended data.The selection of trimming steps and
their associated parameters are supplied on the command line.
The current trimming steps are:
- ILLUMINACLIP: Cut adapter and other illumina-specific sequences from
the read.
- SLIDINGWINDOW: Perform a sliding window trimming, cutting once the
average quality within the window falls below a threshold.
- LEADING: Cut bases off the start of a read, if below a threshold
quality
- TRAILING: Cut bases off the end of a read, if below a threshold
quality
- CROP: Cut the read to a specified length
- HEADCROP: Cut the specified number of bases from the start of the
read
- MINLEN: Drop the read if it is below a specified length
- TOPHRED33: Convert quality scores to Phred-33
- TOPHRED64: Convert quality scores to Phred-64
It works with FASTQ (using phred + 33 or phred + 64 quality scores,
depending on the Illumina pipeline used), either uncompressed or
gzipp'ed FASTQ. Use of gzip format is determined based on the .gz
extension.
For single-ended data, one input and one output file are specified,
plus the processing steps. For paired-end data, two input files are
specified, and 4 output files, 2 for the 'paired' output where both
reads survived the processing, and 2 for corresponding 'unpaired'
output where a read survived, but the partner read did not.
Citations
Bolger, A. M., Lohse, M., & Usadel, B. (2014).
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bioinformatics, btu170.